Job ID = 2590223 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,014,296 reads read : 50,028,592 reads written : 25,014,296 reads 0-length : 25,014,296 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:44 25014296 reads; of these: 25014296 (100.00%) were unpaired; of these: 5514570 (22.05%) aligned 0 times 16171838 (64.65%) aligned exactly 1 time 3327888 (13.30%) aligned >1 times 77.95% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 7031385 / 19499726 = 0.3606 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 20:25:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 20:25:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:25:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:25:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 20:25:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:25:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:25:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 20:25:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:25:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:25:15: 1000000 INFO @ Mon, 12 Aug 2019 20:25:16: 1000000 INFO @ Mon, 12 Aug 2019 20:25:17: 1000000 INFO @ Mon, 12 Aug 2019 20:25:21: 2000000 INFO @ Mon, 12 Aug 2019 20:25:25: 2000000 INFO @ Mon, 12 Aug 2019 20:25:26: 2000000 INFO @ Mon, 12 Aug 2019 20:25:28: 3000000 INFO @ Mon, 12 Aug 2019 20:25:34: 3000000 INFO @ Mon, 12 Aug 2019 20:25:35: 4000000 INFO @ Mon, 12 Aug 2019 20:25:35: 3000000 INFO @ Mon, 12 Aug 2019 20:25:41: 5000000 INFO @ Mon, 12 Aug 2019 20:25:43: 4000000 INFO @ Mon, 12 Aug 2019 20:25:44: 4000000 INFO @ Mon, 12 Aug 2019 20:25:48: 6000000 INFO @ Mon, 12 Aug 2019 20:25:52: 5000000 INFO @ Mon, 12 Aug 2019 20:25:53: 5000000 INFO @ Mon, 12 Aug 2019 20:25:55: 7000000 INFO @ Mon, 12 Aug 2019 20:26:01: 6000000 INFO @ Mon, 12 Aug 2019 20:26:02: 8000000 INFO @ Mon, 12 Aug 2019 20:26:02: 6000000 INFO @ Mon, 12 Aug 2019 20:26:08: 9000000 INFO @ Mon, 12 Aug 2019 20:26:10: 7000000 INFO @ Mon, 12 Aug 2019 20:26:10: 7000000 INFO @ Mon, 12 Aug 2019 20:26:15: 10000000 INFO @ Mon, 12 Aug 2019 20:26:19: 8000000 INFO @ Mon, 12 Aug 2019 20:26:19: 8000000 INFO @ Mon, 12 Aug 2019 20:26:21: 11000000 INFO @ Mon, 12 Aug 2019 20:26:28: 9000000 INFO @ Mon, 12 Aug 2019 20:26:28: 9000000 INFO @ Mon, 12 Aug 2019 20:26:28: 12000000 INFO @ Mon, 12 Aug 2019 20:26:32: #1 tag size is determined as 48 bps INFO @ Mon, 12 Aug 2019 20:26:32: #1 tag size = 48 INFO @ Mon, 12 Aug 2019 20:26:32: #1 total tags in treatment: 12468341 INFO @ Mon, 12 Aug 2019 20:26:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:26:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:26:32: #1 tags after filtering in treatment: 12468341 INFO @ Mon, 12 Aug 2019 20:26:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:26:32: #1 finished! INFO @ Mon, 12 Aug 2019 20:26:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:26:33: #2 number of paired peaks: 438 WARNING @ Mon, 12 Aug 2019 20:26:33: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Mon, 12 Aug 2019 20:26:33: start model_add_line... INFO @ Mon, 12 Aug 2019 20:26:33: start X-correlation... INFO @ Mon, 12 Aug 2019 20:26:33: end of X-cor INFO @ Mon, 12 Aug 2019 20:26:33: #2 finished! INFO @ Mon, 12 Aug 2019 20:26:33: #2 predicted fragment length is 44 bps INFO @ Mon, 12 Aug 2019 20:26:33: #2 alternative fragment length(s) may be 1,44,518,546,577 bps INFO @ Mon, 12 Aug 2019 20:26:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.20_model.r WARNING @ Mon, 12 Aug 2019 20:26:33: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:26:33: #2 You may need to consider one of the other alternative d(s): 1,44,518,546,577 WARNING @ Mon, 12 Aug 2019 20:26:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:26:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:26:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:26:36: 10000000 INFO @ Mon, 12 Aug 2019 20:26:36: 10000000 INFO @ Mon, 12 Aug 2019 20:26:44: 11000000 INFO @ Mon, 12 Aug 2019 20:26:45: 11000000 INFO @ Mon, 12 Aug 2019 20:26:53: 12000000 INFO @ Mon, 12 Aug 2019 20:26:53: 12000000 INFO @ Mon, 12 Aug 2019 20:26:57: #1 tag size is determined as 48 bps INFO @ Mon, 12 Aug 2019 20:26:57: #1 tag size = 48 INFO @ Mon, 12 Aug 2019 20:26:57: #1 total tags in treatment: 12468341 INFO @ Mon, 12 Aug 2019 20:26:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:26:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:26:57: #1 tags after filtering in treatment: 12468341 INFO @ Mon, 12 Aug 2019 20:26:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:26:57: #1 finished! INFO @ Mon, 12 Aug 2019 20:26:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:26:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:26:57: #1 tag size is determined as 48 bps INFO @ Mon, 12 Aug 2019 20:26:57: #1 tag size = 48 INFO @ Mon, 12 Aug 2019 20:26:57: #1 total tags in treatment: 12468341 INFO @ Mon, 12 Aug 2019 20:26:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:26:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:26:58: #1 tags after filtering in treatment: 12468341 INFO @ Mon, 12 Aug 2019 20:26:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:26:58: #1 finished! INFO @ Mon, 12 Aug 2019 20:26:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:26:58: #2 number of paired peaks: 438 WARNING @ Mon, 12 Aug 2019 20:26:58: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Mon, 12 Aug 2019 20:26:58: start model_add_line... INFO @ Mon, 12 Aug 2019 20:26:58: start X-correlation... INFO @ Mon, 12 Aug 2019 20:26:58: end of X-cor INFO @ Mon, 12 Aug 2019 20:26:58: #2 finished! INFO @ Mon, 12 Aug 2019 20:26:58: #2 predicted fragment length is 44 bps INFO @ Mon, 12 Aug 2019 20:26:58: #2 alternative fragment length(s) may be 1,44,518,546,577 bps INFO @ Mon, 12 Aug 2019 20:26:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.10_model.r WARNING @ Mon, 12 Aug 2019 20:26:58: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:26:58: #2 You may need to consider one of the other alternative d(s): 1,44,518,546,577 WARNING @ Mon, 12 Aug 2019 20:26:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:26:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:26:59: #2 number of paired peaks: 438 WARNING @ Mon, 12 Aug 2019 20:26:59: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Mon, 12 Aug 2019 20:26:59: start model_add_line... INFO @ Mon, 12 Aug 2019 20:26:59: start X-correlation... INFO @ Mon, 12 Aug 2019 20:26:59: end of X-cor INFO @ Mon, 12 Aug 2019 20:26:59: #2 finished! INFO @ Mon, 12 Aug 2019 20:26:59: #2 predicted fragment length is 44 bps INFO @ Mon, 12 Aug 2019 20:26:59: #2 alternative fragment length(s) may be 1,44,518,546,577 bps INFO @ Mon, 12 Aug 2019 20:26:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.05_model.r WARNING @ Mon, 12 Aug 2019 20:26:59: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:26:59: #2 You may need to consider one of the other alternative d(s): 1,44,518,546,577 WARNING @ Mon, 12 Aug 2019 20:26:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:26:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:26:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:27:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:27:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:27:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:27:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.20_summits.bed INFO @ Mon, 12 Aug 2019 20:27:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:27:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:27:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:27:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:27:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:27:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.10_summits.bed INFO @ Mon, 12 Aug 2019 20:27:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (526 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:27:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:27:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:27:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709764/SRX5709764.05_summits.bed INFO @ Mon, 12 Aug 2019 20:27:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (792 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。